Increasing water shortages and environmental pollution from excess chemical nitrogen fertilizer use necessitate the development of irrigation-nitrogen conservation technology in oilseed flax production. Therefore, a two-year split-plot design experiment (2017–2018) was conducted with three types of irrigation (I) levels (no irrigation (I0), irrigation of 1200 m3 ha−1 (I1200), and 1800 m3 ha−1 (I1800)) as the main plot and three nitrogen (N) application rates (0 (N0), 60 (N60) and 120 (N120) kg N ha−1) as the subplot in Northwest China to determine the effects of irrigation and N rates on oilseed flax grain yield, yield components, water-use efficiency (WUE), and N partial factor productivity (NPFP). The results show that I1800 optimized the farmland water storage and water storage efficiency (WSE), which gave rise to greater above-ground biomass. Under I1800, the effective capsule (EC) number increased significantly with increasing irrigation amounts, which increased significantly with increasing nitrogen application rate (0–120 kg ha−1). Both irrigation and nitrogen indirectly affect GY by affecting EC; the highest grain yield was observed at the I1800N60 treatment, which increased by 69.04% and 22.80% in 2017 and 2018 compared with the I0N0 treatment, respectively. As a result, both irrigation and N affect grain yield by affecting soil water status, improving above-ground biomass, and finally affecting yield components. In addition, I1800N60 also obtained a higher WUE and the highest NPFP due to a higher grain yield and a lower N application rate. Hence, our study recommends that irrigation with 1800 m3 ha−1 coupled with 60 kg N ha−1 could be a promising strategy for synergistically improving oilseed flax WUE, grain yield and yield components within this semi-arid region.